Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 38
Found at i:1497340 original size:2 final size:2
Alignment explanation
Indices: 1497333--1497357 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1497323 AAATAAAGAA
1497333 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1497358 ATAGTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1499368 original size:85 final size:84
Alignment explanation
Indices: 1499257--1499814 Score: 620
Period size: 85 Copynumber: 6.5 Consensus size: 84
1499247 CTCGACAGAT
* * * *
1499257 TTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGTTGTAAATTTGACATG-CTCTTGAACT
1 TTTTT-TTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTC-CTTGAACT
* *
1499321 GAATGGAATTGAACTCGAAGG
64 GAATGTAATCGAACTCGAAGG
* *
1499342 TATTTTTTGACAAATAACCCTTCTCGCCTTGAGTTATACTGTAAATTTGATATGTCCTT-AAGCT
1 T-TTTTTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAA-CT
1499406 GAATGTAATCGAACTCGAAGG
64 GAATGTAATCGAACTCGAAGG
* * * * * * * * *
1499427 TCTTTGTTGACAGATAACCCTTCTCTCTTTGAGTTGTGTTATAGATTTGATATGTCCTTGAGCTA
1 T-TTTTTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAACTG
1499492 AATGTAATCGAACT-GAAAGG
65 AATGTAATCGAACTCG-AAGG
* * * * * *
1499512 TTTTTATTAATAGATAATCCTTCTCGCCTTGAGTTATGTTGTAAATTTGATATATCCTTGAGCTG
1 TTTTT-TTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAACTG
*
1499577 AATGTAATCGAAGTCGAAGG
65 AATGTAATCGAACTCGAAGG
1499597 TTTTTATTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGA-T
1 TTTTT-TTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGA-ACT
* *
1499661 GAATGTAATCAAACTTGAAGG
64 GAATGTAATCGAACTCGAAGG
* * * * * **
1499682 TTTTGGTTGACAAATAGCCCTTCTCGCCTTGAGCTATGATGTAAATTTGATATGTCCTTGAGTTG
1 TTTT-TTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAACTG
*
1499747 AGTGTAATCGAACTCGAAGG
65 AATGTAATCGAACTCGAAGG
* * * **
1499767 TTTTTTTGCTGGCAGATAGCCCTTTTCGCCTTGAGCCATGCTGTAAAT
1 -TTTTTT--TGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAAT
1499815 AGTTCCTTTA
Statistics
Matches: 404, Mismatches: 56, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
84 6 0.01
85 353 0.87
86 11 0.03
87 34 0.08
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (84 bp):
TTTTTTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAACTGA
ATGTAATCGAACTCGAAGG
Found at i:1499732 original size:255 final size:255
Alignment explanation
Indices: 1499275--1499771 Score: 705
Period size: 255 Copynumber: 1.9 Consensus size: 255
1499265 GACAGATAGC
*
1499275 CCTTCTCGCCTTGAGCTATGTTGTAAATTTGACATGCTCTTGAACTGAATGGAATTGAACTCGAA
1 CCTTCTCGCCTTGAGCTATGTTGTAAATTTGACATGCTCTTGAACTGAATGGAATCGAACTCGAA
*
1499340 GGTATTTTTTGACAAATAACCCTTCTCGCCTTGAGTTATACTGTAAATTTGATATGTCCTTAAGC
66 GGTATTTTTTGACAAATAACCCTTCTCGCCTTGAGTTATACTGTAAATTTGATATGTCCTTAAGA
* * * * * * *
1499405 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCTCTTTGAGTTGTGTTATA
131 TGAATGTAATCAAACTCGAAGGTCTTTGTTGACAAATAACCCTTCTCGCCTTGAGCTATGATATA
*
1499470 GATTTGATATGTCCTTGAGCTAAATGTAATCGAACT-GAAAGGTTTTTATTAATAGATAAT
196 AATTTGATATGTCCTTGAGCTAAATGTAATCGAACTCG-AAGGTTTTTATTAATAGATAAT
* * * * * *
1499530 CCTTCTCGCCTTGAGTTATGTTGTAAATTTGATAT-ATCCTTGAGCTGAATGTAATCGAAGTCGA
1 CCTTCTCGCCTTGAGCTATGTTGTAAATTTGACATGCT-CTTGAACTGAATGGAATCGAACTCGA
* * *
1499594 AGGT-TTTTATTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGA
65 AGGTATTTT-TTGACAAATAACCCTTCTCGCCTTGAGTTATACTGTAAATTTGATATGTCCTTAA
* *
1499658 GATGAATGTAATCAAACTTGAAGGT-TTTGGTTGACAAATAGCCCTTCTCGCCTTGAGCTATGAT
129 GATGAATGTAATCAAACTCGAAGGTCTTT-GTTGACAAATAACCCTTCTCGCCTTGAGCTATGAT
* * * *
1499722 GTAAATTTGATATGTCCTTGAGTTGAGTGTAATCGAACTCGAAGGTTTTT
193 ATAAATTTGATATGTCCTTGAGCTAAATGTAATCGAACTCGAAGGTTTTT
1499772 TTGCTGGCAG
Statistics
Matches: 213, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
254 8 0.04
255 204 0.96
256 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (255 bp):
CCTTCTCGCCTTGAGCTATGTTGTAAATTTGACATGCTCTTGAACTGAATGGAATCGAACTCGAA
GGTATTTTTTGACAAATAACCCTTCTCGCCTTGAGTTATACTGTAAATTTGATATGTCCTTAAGA
TGAATGTAATCAAACTCGAAGGTCTTTGTTGACAAATAACCCTTCTCGCCTTGAGCTATGATATA
AATTTGATATGTCCTTGAGCTAAATGTAATCGAACTCGAAGGTTTTTATTAATAGATAAT
Found at i:1505206 original size:5 final size:5
Alignment explanation
Indices: 1505187--1505299 Score: 114
Period size: 5 Copynumber: 23.4 Consensus size: 5
1505177 ACTAATCTCC
*
1505187 AAAA- AAAA- AAAAT AACAT AAAAT AAAAT AAAAT AAAA- AACAA- ACAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT A-AAAT
* * *
1505235 -AAAT -AAAT AAAAT AAAAT -AAAT AAAAC AAGAT AAAAT AGAAT AGAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT
1505283 AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AA
1505300 GAAAAAGAGG
Statistics
Matches: 94, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
4 22 0.23
5 67 0.71
6 5 0.05
ACGTcount: A:0.78, C:0.04, G:0.03, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:1505418 original size:51 final size:50
Alignment explanation
Indices: 1505336--1505449 Score: 135
Period size: 49 Copynumber: 2.2 Consensus size: 50
1505326 AGAAACAAAA
* *
1505336 AAATAAAAATTAAATTAAATTAAAAAAATAAAACCATGATATATATATATAT
1 AAATAAAAATTAAATTAAATTAAAAAAATAAAA-AATG-TATACATATATAT
*
1505388 ATAATAAAAA-TAAA-TAAA-TAAAAAGGATAAAAAATGTATACATATATAT
1 A-AATAAAAATTAAATTAAATTAAAAA-AATAAAAAATGTATACATATATAT
1505437 AAATAAAACATTA
1 AAATAAAA-ATTA
1505450 TCTGAAGAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
48 7 0.13
49 14 0.25
50 11 0.20
51 10 0.18
52 5 0.09
53 8 0.15
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (50 bp):
AAATAAAAATTAAATTAAATTAAAAAAATAAAAAATGTATACATATATAT
Found at i:1509820 original size:35 final size:35
Alignment explanation
Indices: 1509760--1509828 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
1509750 TATTCTATAT
* * *
1509760 TTTATATTTTTAAATTTTATCTTTAGATTATGTAA
1 TTTAGATTTATAAATTTTATCTTTAGATGATGTAA
*
1509795 TTTAGATTTATAAATTTTATGTTTAGATGATGTA
1 TTTAGATTTATAAATTTTATCTTTAGATGATGTA
1509829 TTATGAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.32, C:0.01, G:0.10, T:0.57
Consensus pattern (35 bp):
TTTAGATTTATAAATTTTATCTTTAGATGATGTAA
Found at i:1510619 original size:18 final size:19
Alignment explanation
Indices: 1510590--1510625 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1510580 TATTAATATA
*
1510590 TTTATGTAAATATTATTTT
1 TTTATGTAAATAATATTTT
1510609 TTTAT-TAAATAATATTT
1 TTTATGTAAATAATATTT
1510626 ATATATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTATGTAAATAATATTTT
Found at i:1512369 original size:21 final size:21
Alignment explanation
Indices: 1512339--1512386 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1512329 GCAGGGGTAC
* *
1512339 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
1512360 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
1512381 ATGCCA
1 ATGCCA
1512387 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:1512416 original size:21 final size:21
Alignment explanation
Indices: 1512390--1512483 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
1512380 TATGCCATCT
* *
1512390 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
1512411 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
*
1512432 CCGCCA-TGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
1512453 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
1512474 CCGCAGGGTT
1 CCGCAGGGTT
1512484 TTATACCATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.26, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:1513065 original size:33 final size:34
Alignment explanation
Indices: 1513006--1513102 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 34
1512996 AAATGTTTTT
*
1513006 AAAATACAAATTATATTATTCAAAATTTAAAATA
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
1513040 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
1513073 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCAAAATTTAA
1513103 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCAAAATTTAAAATA
Found at i:1513109 original size:34 final size:32
Alignment explanation
Indices: 1513004--1513109 Score: 122
Period size: 34 Copynumber: 3.2 Consensus size: 32
1512994 ATAAATGTTT
*
1513004 TTAAAATACAAATTATATTATTCAAAATTTAAAA
1 TTAAAATAAAAATTATATTATTC-AAATTT-AAA
* *
1513038 TAAAAATAAAAATAATATTATTCAAATTTAAA
1 TTAAAATAAAAATTATATTATTCAAATTTAAA
* *
1513070 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTC-AAATTTAA-A
1513105 TTAAA
1 TTAAA
1513110 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (32 bp):
TTAAAATAAAAATTATATTATTCAAATTTAAA
Found at i:1513734 original size:128 final size:128
Alignment explanation
Indices: 1513506--1514115 Score: 1179
Period size: 128 Copynumber: 4.8 Consensus size: 128
1513496 CCTGATTTAC
*
1513506 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGTAATGATAACATATTCTCTGA
1 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
1513571 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAA
66 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAA
1513634 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
1 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
*
1513699 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGTAA
66 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAA
1513762 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGAT-ACATATTCTCTGA
1 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
1513826 CGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAA
66 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAA
1513888 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
1 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
1513953 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAA
66 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAA
*
1514016 TGATATATCTAGTGTCTCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
1 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
1514081 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCC
66 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCC
1514116 CCCCCGGGAA
Statistics
Matches: 476, Mismatches: 4, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
126 93 0.20
127 64 0.13
128 319 0.67
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (128 bp):
TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAA
Found at i:1513957 original size:254 final size:256
Alignment explanation
Indices: 1513506--1514115 Score: 1179
Period size: 254 Copynumber: 2.4 Consensus size: 256
1513496 CCTGATTTAC
*
1513506 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGTAATGATAACATATTCTCTGA
1 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
1513571 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATG
66 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATG
1513636 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG
131 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG
1513701 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGTAA
196 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGTAA
1513762 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGAT-ACATATTCTCTGA
1 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
1513826 CGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATG
66 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATG
1513890 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG
131 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG
*
1513955 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAA
196 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGTAA
*
1514016 TGATATATCTAGTGTCTCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
1 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
1514081 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCC
66 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCC
1514116 CCCCCGGGAA
Statistics
Matches: 349, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
254 220 0.63
255 64 0.18
256 65 0.19
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (256 bp):
TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAATG
ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG
AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGTAA
Found at i:1514114 original size:16 final size:16
Alignment explanation
Indices: 1514090--1514131 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1514080 ACGAAATAAT
* *
1514090 GGAAGGCGCGCCCCCG
1 GGAACGCGCCCCCCCG
1514106 GGAACGCGCCCCCCCG
1 GGAACGCGCCCCCCCG
1514122 GGAACGCGCC
1 GGAACGCGCC
1514132 TTCATGTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.14, C:0.48, G:0.38, T:0.00
Consensus pattern (16 bp):
GGAACGCGCCCCCCCG
Found at i:1520253 original size:28 final size:28
Alignment explanation
Indices: 1520213--1520322 Score: 107
Period size: 28 Copynumber: 3.9 Consensus size: 28
1520203 AGGGATACTG
* *
1520213 GTTTCAAGAGAAACCGACTCAAAGATAA
1 GTTTCAAAAGAAACAGACTCAAAGATAA
**
1520241 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATAA
* * **
1520269 GTTTCAAGAA-AAATAAACTCAAAGATTT
1 GTTTCAA-AAGAAACAGACTCAAAGATAA
*
1520297 GTTTCAAGAA-AAACAAACTCAAAGAT
1 GTTTCAA-AAGAAACAGACTCAAAGAT
1520323 GATGTGTTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
28 72 0.97
29 2 0.03
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.23
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGACTCAAAGATAA
Found at i:1520508 original size:65 final size:65
Alignment explanation
Indices: 1520428--1520586 Score: 180
Period size: 67 Copynumber: 2.4 Consensus size: 65
1520418 CAAAGATGGT
1520428 AAAATTTGTTTCCAAAGAAA-AAGACTCAAA-GATT-TTTGTCAAAAGAAACTGTATCAAGAGAG
1 AAAATTTGTTTCCAAAGAAACAA-ACTCAAATG-TTGTTTGTCAAAAGAAACTGTATCAAGAGAG
1520490 AC
64 AC
* * ** * *
1520492 AAAATTTTGTTTCCAAAGAAACAATCTCAAATGTTGGTTTTTCATTAGAATCTGTCTCAAGAGAG
1 AAAA-TTTGTTTCCAAAGAAACAAACTCAAATGTT-GTTTGTCAAAAGAAACTGTATCAAGAGAG
1520557 AC
64 AC
** *
1520559 AAAATTTGTTTTTAAAGAAATAAACTCA
1 AAAATTTGTTTCCAAAGAAACAAACTCA
1520587 CAAATGATTT
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
64 4 0.05
65 24 0.30
66 23 0.29
67 29 0.36
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.31
Consensus pattern (65 bp):
AAAATTTGTTTCCAAAGAAACAAACTCAAATGTTGTTTGTCAAAAGAAACTGTATCAAGAGAGAC
Found at i:1529201 original size:3 final size:3
Alignment explanation
Indices: 1529182--1529215 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1529172 TAAAAATGTA
* *
1529182 AAT AAT GAT ATT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1529216 TAAAAAGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1532501 original size:16 final size:16
Alignment explanation
Indices: 1532480--1532528 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
1532470 TAATAAATAA
1532480 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1532496 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1532512 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1532528 A
1 A
1532529 AATTTTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1532659 original size:23 final size:23
Alignment explanation
Indices: 1532602--1532682 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
1532592 ATAAACGAAC
*
1532602 ATAAATGAACGTAAACGAACACA
1 ATAAATGAACATAAACGAACACA
* *
1532625 A-ACGAATGAACATAAACGAGCATA
1 ATA--AATGAACATAAACGAACACA
*
1532649 ATAAATGAACATAAATGAACACA
1 ATAAATGAACATAAACGAACACA
*
1532672 ATAAACGAACA
1 ATAAATGAACA
1532683 ACACAAACAC
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
22 1 0.02
23 28 0.58
24 18 0.38
25 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.12, T:0.14
Consensus pattern (23 bp):
ATAAATGAACATAAACGAACACA
Found at i:1533008 original size:24 final size:22
Alignment explanation
Indices: 1532947--1533040 Score: 115
Period size: 24 Copynumber: 4.3 Consensus size: 22
1532937 CCTTCTGTTC
1532947 GAACATAAATGAAG--ATAAAT
1 GAACATAAATGAAGACATAAAT
1532967 GAACATAAATG-A-ACATAAAT
1 GAACATAAATGAAGACATAAAT
*
1532987 GAACATAAATGAATGGATATAAAT
1 GAACATAAATGAA--GACATAAAT
1533011 GAACATAAATGAACGAACATAAAT
1 GAACATAAATGAA-G-ACATAAAT
1533035 GAACAT
1 GAACAT
1533041 TTAATCGAAC
Statistics
Matches: 64, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
19 1 0.02
20 28 0.44
21 1 0.02
23 1 0.02
24 33 0.52
ACGTcount: A:0.57, C:0.09, G:0.14, T:0.20
Consensus pattern (22 bp):
GAACATAAATGAAGACATAAAT
Found at i:1533028 original size:14 final size:14
Alignment explanation
Indices: 1533011--1533038 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1533001 GGATATAAAT
1533011 GAACATAAATGAAC
1 GAACATAAATGAAC
1533025 GAACATAAATGAAC
1 GAACATAAATGAAC
1533039 ATTTAATCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (14 bp):
GAACATAAATGAAC
Found at i:1533040 original size:10 final size:10
Alignment explanation
Indices: 1532947--1533024 Score: 102
Period size: 10 Copynumber: 7.4 Consensus size: 10
1532937 CCTTCTGTTC
1532947 GAACATAAAT
1 GAACATAAAT
*
1532957 GAAGATAAAT
1 GAACATAAAT
1532967 GAACATAAAT
1 GAACATAAAT
1532977 GAACATAAAT
1 GAACATAAAT
1532987 GAACATAAAT
1 GAACATAAAT
*
1532997 GAATGGATATAAAT
1 G-A---ACATAAAT
1533011 GAACATAAAT
1 GAACATAAAT
1533021 GAAC
1 GAAC
1533025 GAACATAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
10 50 0.83
11 1 0.02
13 1 0.02
14 8 0.13
ACGTcount: A:0.58, C:0.08, G:0.14, T:0.21
Consensus pattern (10 bp):
GAACATAAAT
Found at i:1534517 original size:2 final size:2
Alignment explanation
Indices: 1534512--1534561 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1534502 ACACACACAC
1534512 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1534554 AT AT AT AT
1 AT AT AT AT
1534562 TAATTGTATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1536053 original size:2 final size:2
Alignment explanation
Indices: 1536046--1536079 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1536036 ACACTAAGAC
1536046 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1536080 GATTAATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1537480 original size:36 final size:36
Alignment explanation
Indices: 1537375--1537482 Score: 173
Period size: 36 Copynumber: 3.0 Consensus size: 36
1537365 TGATCTGATC
1537375 TTGCTTCACTACTCTTTTTGTGAAGGCTGGATTTG-CA
1 TTGCTTCACTACTC-TTTTGTGAAGGCTGGA-TTGACA
* *
1537412 TTGTTTCACTACTCTTTTGTGAAGGCCGGATTGACA
1 TTGCTTCACTACTCTTTTGTGAAGGCTGGATTGACA
1537448 TTGCTTCACTACTCTTTTGTGAAGGCTGGATTGAC
1 TTGCTTCACTACTCTTTTGTGAAGGCTGGATTGAC
1537483 TTGGAAAGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
35 3 0.05
36 50 0.76
37 13 0.20
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.41
Consensus pattern (36 bp):
TTGCTTCACTACTCTTTTGTGAAGGCTGGATTGACA
Found at i:1537605 original size:89 final size:89
Alignment explanation
Indices: 1537448--1537739 Score: 451
Period size: 89 Copynumber: 3.3 Consensus size: 89
1537438 CGGATTGACA
* * ** * * *
1537448 TTGCTT-CACTACTCTTTTGTGAAGGCTGGATTGACTTGGAAAGAATCGGTTTCACTACTCTTCC
1 TTGCTTCCACTACTCTTCTGTGGAGATTGGATGGACTTGGAAAGAATCTGTTTTACTACTCTTCC
*
1537512 GTGAAGATCATATTCAATGTTGAT
66 GTGAAGATCAGATTCAATGTTGAT
* * * **
1537536 TTGCTTCCACTACTCTTCTGTGGAGATTGGATGGATTTGGAAAGAATATATTTTACTACTCTTTT
1 TTGCTTCCACTACTCTTCTGTGGAGATTGGATGGACTTGGAAAGAATCTGTTTTACTACTCTTCC
1537601 GTGAAGATCAGATTCAATGTTGAT
66 GTGAAGATCAGATTCAATGTTGAT
1537625 TTGCTTCCACTACTCTTCTGTGGAGATTGGATGGACTTGGAAAGAATCTGTTTTACTACTCTTCC
1 TTGCTTCCACTACTCTTCTGTGGAGATTGGATGGACTTGGAAAGAATCTGTTTTACTACTCTTCC
1537690 GTGAAGATCAGATTCAATGTTGAT
66 GTGAAGATCAGATTCAATGTTGAT
*
1537714 TTGCTTCCACTACTCTTCCGTGGAGA
1 TTGCTTCCACTACTCTTCTGTGGAGA
1537740 CCAAATCTAC
Statistics
Matches: 184, Mismatches: 19, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
88 6 0.03
89 178 0.97
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.38
Consensus pattern (89 bp):
TTGCTTCCACTACTCTTCTGTGGAGATTGGATGGACTTGGAAAGAATCTGTTTTACTACTCTTCC
GTGAAGATCAGATTCAATGTTGAT
Found at i:1537641 original size:43 final size:43
Alignment explanation
Indices: 1537500--1537731 Score: 135
Period size: 43 Copynumber: 5.3 Consensus size: 43
1537490 GAATCGGTTT
* *
1537500 CACTACTCTTCCGTGAAGATCATATTCAATGTTGATTTGCTTC
1 CACTACTCTTCTGTGAAGATCAGATTCAATGTTGATTTGCTTC
* ** ** * ** * * *
1537543 CACTACTCTTCTGTGGAGATTGGATGGATTTGGAAAGAATAT-ATTT
1 CACTACTCTTCTGTGAAGATCAGATTCA-AT-G-TTG-ATTTGCTTC
* *
1537589 TACTACTCTTTTGTGAAGATCAGATTCAATGTTGATTTGCTTC
1 CACTACTCTTCTGTGAAGATCAGATTCAATGTTGATTTGCTTC
* ** ** * ** * *
1537632 CACTACTCTTCTGTGGAGATTGGATGGACTTGGAAAGAATCTG-TTT
1 CACTACTCTTCTGTGAAGATCAGATTCA-AT-G-TTG-ATTTGCTTC
* *
1537678 TACTACTCTTCCGTGAAGATCAGATTCAATGTTGATTTGCTTC
1 CACTACTCTTCTGTGAAGATCAGATTCAATGTTGATTTGCTTC
1537721 CACTACTCTTC
1 CACTACTCTTC
1537732 CGTGGAGACC
Statistics
Matches: 128, Mismatches: 51, Indels: 20
0.64 0.26 0.10
Matches are distributed among these distances:
42 7 0.05
43 58 0.45
44 4 0.03
45 4 0.03
46 48 0.38
47 7 0.05
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (43 bp):
CACTACTCTTCTGTGAAGATCAGATTCAATGTTGATTTGCTTC
Found at i:1542460 original size:45 final size:45
Alignment explanation
Indices: 1542340--1542446 Score: 173
Period size: 45 Copynumber: 2.4 Consensus size: 45
1542330 GGTTCACTAA
*
1542340 GAGTGCATCGATACATAAAATGCATTCGATGTTTTAAACAAGCCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTAAACAAGCCT
1542385 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AA-CCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTT-A-AACAAGCCT
1542430 GAGTGCATCGATGCATA
1 GAGTGCATCGATGCATA
1542447 GTAGTGCATC
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
45 54 0.92
46 3 0.05
47 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (45 bp):
GAGTGCATCGATGCATAAAATGCATTCGATGTTTTAAACAAGCCT
Found at i:1542476 original size:18 final size:18
Alignment explanation
Indices: 1542433--1542477 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1542423 AAAACCTGAG
* *
1542433 TGCATCGATGCATAGTAG
1 TGCATCGATGCATAGAAA
1542451 TGCATCGATGCATA-AAA
1 TGCATCGATGCATAGAAA
1542468 TGCATTCGAT
1 TGCA-TCGAT
1542478 ATGGTGAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (18 bp):
TGCATCGATGCATAGAAA
Found at i:1550419 original size:8 final size:8
Alignment explanation
Indices: 1550327--1550421 Score: 53
Period size: 8 Copynumber: 12.5 Consensus size: 8
1550317 AAATTTTACT
1550327 TAATA-TA
1 TAATATTA
*
1550334 TCATATTA
1 TAATATTA
1550342 TAA-A-TA
1 TAATATTA
*
1550348 TAA-ATAA
1 TAATATTA
*
1550355 TATTATTA
1 TAATATTA
1550363 TAATATTA
1 TAATATTA
*
1550371 AAATAGATTAA
1 TAAT--ATT-A
1550382 TAATA--A
1 TAATATTA
*
1550388 TAAT-TCA
1 TAATATTA
1550395 TAATATTA
1 TAATATTA
1550403 TAA-ATTA
1 TAATATTA
*
1550410 TAATAGTA
1 TAATATTA
1550418 TAAT
1 TAAT
1550422 TAATCCTATA
Statistics
Matches: 68, Mismatches: 10, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
6 11 0.16
7 20 0.29
8 29 0.43
9 1 0.01
10 3 0.04
11 4 0.06
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (8 bp):
TAATATTA
Found at i:1552109 original size:83 final size:84
Alignment explanation
Indices: 1551957--1552159 Score: 225
Period size: 83 Copynumber: 2.4 Consensus size: 84
1551947 CGTTTTTCTA
* * * * * * * ** *
1551957 AAAACGCCGCAATAGTG-TGTTAATTAGCGGCGTTTATATCACAAACGCTTCAATAGATTATAAA
1 AAAACGCCGCAATAGAGCTGTAAACTGGCAGCGTTTTTACCACAAACGCCACAATAGAGTATAAA
* *
1552021 ATTTTGCGGCGATTTAG-C
66 ATTTTGCAGCGATTGAGTC
*
1552039 TAAAACGCCGCAATATAG-TGGTAAACTGGCAGCGTTTTTACCACAAACGCCACAATAGAGTAT-
1 -AAAACGCCGCAATAGAGCT-GTAAACTGGCAGCGTTTTTACCACAAACGCCACAATAGAGTATA
1552102 AAATTTTGCAGCGATTGAGTC
64 AAATTTTGCAGCGATTGAGTC
* *
1552123 AAAACGCCGCAATAGAGCTGTAAATTGGCGGCGTTTT
1 AAAACGCCGCAATAGAGCTGTAAACTGGCAGCGTTTT
1552160 GACAAAAAAT
Statistics
Matches: 101, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
83 65 0.64
84 36 0.36
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (84 bp):
AAAACGCCGCAATAGAGCTGTAAACTGGCAGCGTTTTTACCACAAACGCCACAATAGAGTATAAA
ATTTTGCAGCGATTGAGTC
Found at i:1552178 original size:83 final size:84
Alignment explanation
Indices: 1552007--1552178 Score: 206
Period size: 83 Copynumber: 2.1 Consensus size: 84
1551997 ACAAACGCTT
* * * *
1552007 CAATAGATTATAAAATTTTGCGGCGATTTAGCTAAAACGCCGCAATATAGTGGTAAACTGGCAGC
1 CAATAGAGTATAAAATTTTGCAGCGATTGAGCTAAAACGCCGCAATAGAGTGGTAAACTGGCAGC
* * *
1552072 GTTTTTACCACAAACGCCA
66 GTTTTGACAAAAAACGCCA
* *
1552091 CAATAGAGTAT-AAATTTTGCAGCGATTGAG-TCAAAACGCCGCAATAGAGCT-GTAAATTGGCG
1 CAATAGAGTATAAAATTTTGCAGCGATTGAGCT-AAAACGCCGCAATAGAG-TGGTAAACTGGCA
* *
1552153 GCGTTTTGACAAAAAATGCCG
64 GCGTTTTGACAAAAAACGCCA
1552174 CAATA
1 CAATA
1552179 TATTACACAT
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
82 1 0.01
83 63 0.84
84 11 0.15
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (84 bp):
CAATAGAGTATAAAATTTTGCAGCGATTGAGCTAAAACGCCGCAATAGAGTGGTAAACTGGCAGC
GTTTTGACAAAAAACGCCA
Found at i:1554932 original size:8 final size:8
Alignment explanation
Indices: 1554919--1554944 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1554909 AGCTGATTAG
1554919 GGGCAAGT
1 GGGCAAGT
1554927 GGGCAAGT
1 GGGCAAGT
1554935 GGGCAAGT
1 GGGCAAGT
1554943 GG
1 GG
1554945 CGTTAGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.54, T:0.12
Consensus pattern (8 bp):
GGGCAAGT
Found at i:1555934 original size:23 final size:21
Alignment explanation
Indices: 1555842--1555937 Score: 93
Period size: 21 Copynumber: 4.6 Consensus size: 21
1555832 GCAAGGGAAA
* *
1555842 CAGAGAGAGCAGCAGCGGAAG
1 CAGAGAGAGAAGCAGCGGCAG
** * *
1555863 CAGCTAGAGCAGCAGCGGAAG
1 CAGAGAGAGAAGCAGCGGCAG
*
1555884 CAGAGAGGGAAGCAGCGGCAG
1 CAGAGAGAGAAGCAGCGGCAG
* *
1555905 CACAGAGAGAGGCAGCGGCAG
1 CAGAGAGAGAAGCAGCGGCAG
* *
1555926 AACAGAGAGAAG
1 CAGAGAGAGAAG
1555938 TAATATATCA
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 63 1.00
ACGTcount: A:0.38, C:0.20, G:0.42, T:0.01
Consensus pattern (21 bp):
CAGAGAGAGAAGCAGCGGCAG
Found at i:1563177 original size:198 final size:201
Alignment explanation
Indices: 1562839--1563238 Score: 770
Period size: 198 Copynumber: 2.0 Consensus size: 201
1562829 CCCTTCTCAA
1562839 GTGTTCAACGTGTTCCTCCAAGGTCTTACTATATACCACAATATCATCAAGGTAAACTATAACAA
1 GTGTTCAACGTGTTCCTCCAAGGTCTTACTATATACCACAATATCATCAAGGTAAACTATAACAA
1562904 AACGATCAAGAAAGGGTTATAATACCTTATTCATTAACGTTCAGAATGTAGTAGGGGCATTTGTG
66 AACGATCAAGAAAGGGTTATAATACCTTATTCATTAACGTTCAGAATGTAGTAGGGGCATTTGTG
1562969 AGGCCAAAGGGCA-CACAAGAAACTCATAT-AACCATAGCGTGTCACACAAGCAA-TTCGGTTCA
131 AGGCCAAAGGGCATCACAAGAAACTCATATAAACCATAGCGTGTCACACAAGCAACTTCGGTTCA
1563031 TTGCCT
196 TTGCCT
1563037 GTGTTCAACGTGTTCCTCCAAGGTCTTACTATATACCACAATATCATCAAGGTAAACTATAACAA
1 GTGTTCAACGTGTTCCTCCAAGGTCTTACTATATACCACAATATCATCAAGGTAAACTATAACAA
1563102 AACGATCAAGAAAGGGTTATAATACCTTATTCATTAACGTTCAGAATGTAGTAGGGGCATTTGTG
66 AACGATCAAGAAAGGGTTATAATACCTTATTCATTAACGTTCAGAATGTAGTAGGGGCATTTGTG
1563167 AGGCCAAAGGGCATCACAAGAAACTCATATAAACCATAGCGTGTCACACAAGCAATCTTCGGTTC
131 AGGCCAAAGGGCATCACAAGAAACTCATATAAACCATAGCGTGTCACACAAGCAA-CTTCGGTTC
1563232 ATTGCCT
195 ATTGCCT
1563239 TCAGTTATCC
Statistics
Matches: 198, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
198 143 0.72
199 16 0.08
200 24 0.12
202 15 0.08
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (201 bp):
GTGTTCAACGTGTTCCTCCAAGGTCTTACTATATACCACAATATCATCAAGGTAAACTATAACAA
AACGATCAAGAAAGGGTTATAATACCTTATTCATTAACGTTCAGAATGTAGTAGGGGCATTTGTG
AGGCCAAAGGGCATCACAAGAAACTCATATAAACCATAGCGTGTCACACAAGCAACTTCGGTTCA
TTGCCT
Found at i:1568883 original size:417 final size:416
Alignment explanation
Indices: 1568302--1569073 Score: 1165
Period size: 419 Copynumber: 1.9 Consensus size: 416
1568292 ATATTTTAAT
* * * *
1568302 TATAGTGATAAAATATATTGTCACAAAGATTTTCCTCCATTTGTTTTGCGCCAAAAAAGTCATAT
1 TATAGTAACAAAATATATTGTCACAAAGATTTTCCTCCATTTGTTTTGAGCCAAAAAAATCATAT
* *
1568367 GGTGACAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAACATTGCAACAAAAAATAATG
66 AGTAACAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAACATTGCAACAAAAAATAATG
* *
1568432 AAATTCACATTTTTGTGACAAATTATATTTGTAGTTATAAATTTTAACTATAGTGAT-ATCATAT
131 AAATTCACATTTTTGTGACAAATTATACTTGTAGTTATAAATTTCAACTATAGTGATGA-CATAT
*** * * * * *
1568496 ATTTTTATAACTATTTTTCTGC-ACTTTTTTGTTTC-AAAAGTTATATTGACAATTTTTATAATT
195 ACAATGATAAATATTTTTCTCCAACTTTTTTGTTTCAAAAAGTGATATTGACAAGTTTTATAATT
* *
1568559 ATAATTTATAGTTATTTTTATAGAAAAAATTATCACATCAAATAATAAAATTCAAGTTTTTTGTA
260 ATAATTTATAGTTATTGTTATAGAAAAAATTATCACATCAAATAATAAAATTAAAGTTTTTTGTA
1568624 ATAAATTATTTCTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCATAACTATTTCT
325 ATAAATTATTTCTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCATAACTATTTCT
1568689 CCATAATTTTTAGTGTAAAATATGTTA
390 CCATAATTTTTAGTGTAAAATATGTTA
* *
1568716 TATAGTAACAAAATATATTGTCATAAAGATTTTCCTCCATATTTTTTTGAGCCAAAAAAAATCAT
1 TATAGTAACAAAATATATTGTCACAAAGATTTTCCTCCAT-TTGTTTTGAGCC-AAAAAAATCAT
* ** * *
1568781 ATAGTAATATTTTTTGTAACTATAAGTGTTTATAATTATTACAAAATATATTGTC-ACAAAAAAT
64 ATAGTAACAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAA-ACATTG-CAACAAAAAAT
* *
1568845 AATGATATTCACATTTTTGTGACAAATTATACTTGTAGTTATAAATTTCAATTATAGTGATGACA
127 AATGAAATTCACATTTTTGTGACAAATTATACTTGTAGTTATAAATTTCAACTATAGTGATGACA
* * *
1568910 TATACAATGATAAATATTTTTCTCCAATTTTTTTGTTTCAAAAAGTGATATTGATAAGTTTTGTA
192 TATACAATGATAAATATTTTTCTCCAACTTTTTTGTTTCAAAAAGTGATATTGACAAGTTTTATA
*
1568975 ATTATAATTTATAGTTATTGTTATAGAAAAAATTATCACATCATATAATAAAATTAAAGTTTTTT
257 ATTATAATTTATAGTTATTGTTATAGAAAAAATTATCACATCAAATAATAAAATTAAAGTTTTTT
* * *
1569040 GTAATCAATTATTTTTGTAGTTATATATTTTAAT
322 GTAATAAATTATTTCTGTACTTATATATTTTAAT
1569074 AACAACAACA
Statistics
Matches: 317, Mismatches: 34, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
414 37 0.12
415 10 0.03
416 50 0.16
417 92 0.29
418 14 0.04
419 114 0.36
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.44
Consensus pattern (416 bp):
TATAGTAACAAAATATATTGTCACAAAGATTTTCCTCCATTTGTTTTGAGCCAAAAAAATCATAT
AGTAACAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAACATTGCAACAAAAAATAATG
AAATTCACATTTTTGTGACAAATTATACTTGTAGTTATAAATTTCAACTATAGTGATGACATATA
CAATGATAAATATTTTTCTCCAACTTTTTTGTTTCAAAAAGTGATATTGACAAGTTTTATAATTA
TAATTTATAGTTATTGTTATAGAAAAAATTATCACATCAAATAATAAAATTAAAGTTTTTTGTAA
TAAATTATTTCTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCATAACTATTTCTC
CATAATTTTTAGTGTAAAATATGTTA
Found at i:1571491 original size:3 final size:3
Alignment explanation
Indices: 1571483--1571519 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1571473 TCTTCATTTT
*
1571483 CAC CAC CAC CAC CAC CAC TAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC C
1571520 GTTATTATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.65, G:0.00, T:0.03
Consensus pattern (3 bp):
CAC
Found at i:1571675 original size:20 final size:19
Alignment explanation
Indices: 1571637--1571681 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1571627 GAAAAACTCA
*
1571637 ATAAAAATATCTTACAATT
1 ATAAAAATATCTTAAAATT
*
1571656 ATAAAAATATTTTATAAATT
1 ATAAAAATATCTTA-AAATT
*
1571676 TTAAAA
1 ATAAAA
1571682 GTAGGAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAAAATATCTTAAAATT
Found at i:1574561 original size:32 final size:33
Alignment explanation
Indices: 1574523--1574598 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 33
1574513 TAATAATTTA
**
1574523 TAACAAATATTAATTTCTCATTATAA-AAATTG
1 TAACAAATATTAATTTCTCACAATAACAAATTG
* * * *
1574555 TGACAAATAATATTTTTTCACAATAACAAATTG
1 TAACAAATATTAATTTCTCACAATAACAAATTG
1574588 TAACAAA-ATTA
1 TAACAAATATTA
1574599 TTTAGTCTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 23 0.66
33 12 0.34
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.37
Consensus pattern (33 bp):
TAACAAATATTAATTTCTCACAATAACAAATTG
Found at i:1585593 original size:81 final size:81
Alignment explanation
Indices: 1585491--1585938 Score: 618
Period size: 81 Copynumber: 5.5 Consensus size: 81
1585481 AATTTAACTT
* * * * *
1585491 TTCATCTAACTTG-CATGATTGACACTCTTT-TGCCAAATACACAGA-TATGCCATTTATCCTTT
1 TTCATCTAAC-TGACATAATTGACAC-CTTTCTGCCAAATGCACA-ACTAGGCCATGTATCTTTT
1585553 ACTCAACGGTCTTTAACCG
63 ACTCAACGGTCTTTAACCG
* *
1585572 TTCATCTAACTGACATAATTGACACCTTTATGTCAAATGCACAACTAGGCCATGTATCTTTTACT
1 TTCATCTAACTGACATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATGTATCTTTTACT
*
1585637 CAACGATCTTTAACCG
66 CAACGGTCTTTAACCG
* * *
1585653 TTCATCTAACTCG-CATAATTAACACTTTTCTGCCGAATGCACAACTAGGCCATGTATCTTTTAC
1 TTCATCTAACT-GACATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATGTATCTTTTAC
* *
1585717 TCAACGATCTTTAATCG
65 TCAACGGTCTTTAACCG
* * *
1585734 TTCATCTAACT-AGCATAATTGACACCTTTCTGTCGAATGCACAGCTAGGCCATGTATCTTTTAC
1 TTCATCTAACTGA-CATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATGTATCTTTTAC
1585798 TCAACGGTCTTTAACCG
65 TCAACGGTCTTTAACCG
* *
1585815 TTCATCTAACTGACATAATTGACACCTTTCTGCCAAATGCACAACTAGGACATGTATCTTTTACG
1 TTCATCTAACTGACATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATGTATCTTTTACT
*
1585880 CAATGGTCTTTAACCG
66 CAACGGTCTTTAACCG
* * *
1585896 TTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACA
1 TTCATCTAACTGACATAATTGACACCTTTCTGCCAAATGCACA
1585939 GTTAGGCCTC
Statistics
Matches: 332, Mismatches: 28, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
80 7 0.02
81 323 0.97
82 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (81 bp):
TTCATCTAACTGACATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATGTATCTTTTACT
CAACGGTCTTTAACCG
Found at i:1585893 original size:243 final size:243
Alignment explanation
Indices: 1585491--1585938 Score: 700
Period size: 243 Copynumber: 1.8 Consensus size: 243
1585481 AATTTAACTT
* * * *
1585491 TTCATCTAACTTGCATGATTGACACTCTTTTGCCAAATACACAGATATGCCATTTATCCTTTACT
1 TTCATCTAACTAGCATAATTGACACTCTTTTGCCAAATACACAGATAGGCCATGTATCCTTTACT
*
1585556 CAACGGTCTTTAACCGTTCATCTAACTGACATAATTGACACCTTTATGTCAAATGCACAACTAGG
66 CAACGGTCTTTAACCGTTCATCTAACTGACATAATTGACACCTTTATGCCAAATGCACAACTAGG
* * *
1585621 CCATGTATCTTTTACTCAACGATCTTTAACCGTTCATCTAACTCGCATAATTAACACTTTTCTGC
131 ACATGTATCTTTTACGCAACGATCTTTAACCGTTCATCTAACTCGCATAATTAACACATTTCTGC
*
1585686 CGAATGCACAACTAGGCCATGTATCTTTTACTCAACGATCTTTAATCG
196 CAAATGCACAACTAGGCCATGTATCTTTTACTCAACGATCTTTAATCG
* * * * *
1585734 TTCATCTAACTAGCATAATTGACAC-CTTTCTGTCGAATGCACAGCTAGGCCATGTATCTTTTAC
1 TTCATCTAACTAGCATAATTGACACTCTTT-TGCCAAATACACAGATAGGCCATGTATCCTTTAC
*
1585798 TCAACGGTCTTTAACCGTTCATCTAACTGACATAATTGACACCTTTCTGCCAAATGCACAACTAG
65 TCAACGGTCTTTAACCGTTCATCTAACTGACATAATTGACACCTTTATGCCAAATGCACAACTAG
* * * *
1585863 GACATGTATCTTTTACGCAATGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTG
130 GACATGTATCTTTTACGCAACGATCTTTAACCGTTCATCTAACTCGCATAATTAACACATTTCTG
*
1585928 TCAAATGCACA
195 CCAAATGCACA
1585939 GTTAGGCCTC
Statistics
Matches: 184, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
242 4 0.02
243 180 0.98
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (243 bp):
TTCATCTAACTAGCATAATTGACACTCTTTTGCCAAATACACAGATAGGCCATGTATCCTTTACT
CAACGGTCTTTAACCGTTCATCTAACTGACATAATTGACACCTTTATGCCAAATGCACAACTAGG
ACATGTATCTTTTACGCAACGATCTTTAACCGTTCATCTAACTCGCATAATTAACACATTTCTGC
CAAATGCACAACTAGGCCATGTATCTTTTACTCAACGATCTTTAATCG
Found at i:1586293 original size:54 final size:55
Alignment explanation
Indices: 1586225--1586358 Score: 200
Period size: 55 Copynumber: 2.5 Consensus size: 55
1586215 ACATATATTT
* * *
1586225 CACTTAGTATGAATTTCTT-AGTTTGCACACACAGTGCCCATACGGAAATTCATA
1 CACTTAGTAAGAATTTCTTAAGTTTGCACACAAAGTGCCCATACCGAAATTCATA
* *
1586279 CACTTAGTAAGAATTTATTAATTTTGCACACAAAGTGCCCATACCGAAATTCATA
1 CACTTAGTAAGAATTTCTTAAGTTTGCACACAAAGTGCCCATACCGAAATTCATA
1586334 CACTTAGTATAG-ATTTCTTAAGTTT
1 CACTTAGTA-AGAATTTCTTAAGTTT
1586359 TTGCACGCTT
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
54 17 0.24
55 52 0.73
56 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (55 bp):
CACTTAGTAAGAATTTCTTAAGTTTGCACACAAAGTGCCCATACCGAAATTCATA
Found at i:1586740 original size:22 final size:22
Alignment explanation
Indices: 1586699--1586751 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1586689 GAGTCCTCAA
1586699 TATCGATAC--CCATACCATGG
1 TATCGATACTACCATACCATGG
*
1586719 TATCGATACTACCATACTATGG
1 TATCGATACTACCATACCATGG
*
1586741 TACCGATACTA
1 TATCGATACTA
1586752 TGATATGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 9 0.31
22 20 0.69
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.28
Consensus pattern (22 bp):
TATCGATACTACCATACCATGG
Found at i:1586818 original size:20 final size:20
Alignment explanation
Indices: 1586792--1586843 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1586782 TATTTCGAAA
1586792 TGGTATCGATACAT-T-CCTT
1 TGGTATCGATAC-TCTCCCTT
1586811 TCGGTATCGATACTCTCCCTT
1 T-GGTATCGATACTCTCCCTT
1586832 TGGTATCGATAC
1 TGGTATCGATAC
1586844 CGATTGAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.07
20 23 0.77
21 5 0.17
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.38
Consensus pattern (20 bp):
TGGTATCGATACTCTCCCTT
Found at i:1586926 original size:18 final size:18
Alignment explanation
Indices: 1586903--1586938 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1586893 CTATAGTATC
1586903 AGTACTATTCTATCAGTA
1 AGTACTATTCTATCAGTA
1586921 AGTACTATTCTATCAGTA
1 AGTACTATTCTATCAGTA
1586939 CCGATACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (18 bp):
AGTACTATTCTATCAGTA
Found at i:1622774 original size:12 final size:13
Alignment explanation
Indices: 1622757--1622786 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1622747 TTAATTACGA
1622757 AAATTAAAATTT-
1 AAATTAAAATTTG
1622769 AAATTAAAATTTG
1 AAATTAAAATTTG
1622782 AAATT
1 AAATT
1622787 CGATCCGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (13 bp):
AAATTAAAATTTG
Found at i:1623209 original size:16 final size:16
Alignment explanation
Indices: 1623185--1623225 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
1623175 ATAATTGCAC
*
1623185 AATAGCCCTCCCTATA
1 AATATCCCTCCCTATA
1623201 AATATCCCTCCCTATA
1 AATATCCCTCCCTATA
1623217 AATATCCCT
1 AATATCCCT
1623226 TAAAACAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.32, C:0.37, G:0.02, T:0.29
Consensus pattern (16 bp):
AATATCCCTCCCTATA
Found at i:1624347 original size:12 final size:11
Alignment explanation
Indices: 1624314--1624386 Score: 57
Period size: 10 Copynumber: 6.8 Consensus size: 11
1624304 AGAAAACCGA
1624314 AAATAATAT-T
1 AAATAATATAT
* *
1624324 -AGTAATAAAT
1 AAATAATATAT
1624334 AAATAATACTAT
1 AAATAATA-TAT
1624346 AAATAATATAT
1 AAATAATATAT
1624357 -AAT-ATGATAT
1 AAATAAT-ATAT
1624367 AATATAATATA-
1 AA-ATAATATAT
*
1624378 ATATAATAT
1 AAATAATAT
1624387 GTACTATATA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
9 8 0.16
10 15 0.29
11 11 0.22
12 15 0.29
13 2 0.04
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (11 bp):
AAATAATATAT
Found at i:1624366 original size:5 final size:5
Alignment explanation
Indices: 1624353--1624386 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
1624343 TATAAATAAT
*
1624353 ATATA ATATG ATATA ATATA ATATA ATATA ATAT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATAT
1624387 GTACTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:1624444 original size:21 final size:22
Alignment explanation
Indices: 1624420--1624460 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1624410 TATATAACAT
*
1624420 ATATTATAT-TTTTAAAAAACC
1 ATATAATATGTTTTAAAAAACC
*
1624441 ATATAATATGTTTTCAAAAA
1 ATATAATATGTTTTAAAAAA
1624461 TTATATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (22 bp):
ATATAATATGTTTTAAAAAACC
Found at i:1624454 original size:23 final size:23
Alignment explanation
Indices: 1624417--1624460 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1624407 AACTATATAA
* *
1624417 CATATATTATATTTTTAAAAAAC
1 CATATAATATATTTTCAAAAAAC
*
1624440 CATATAATATGTTTTCAAAAA
1 CATATAATATATTTTCAAAAA
1624461 TTATATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (23 bp):
CATATAATATATTTTCAAAAAAC
Found at i:1624466 original size:22 final size:21
Alignment explanation
Indices: 1624419--1624471 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
1624409 CTATATAACA
*
1624419 TATATTATATTTTTAAAAAAC
1 TATATAATATTTTTAAAAAAC
* * *
1624440 CATATAATATGTTTTCAAAAAT
1 TATATAATAT-TTTTAAAAAAC
1624462 TATAT-ATATT
1 TATATAATATT
1624472 ATATATGTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 1 0.04
21 12 0.46
22 13 0.50
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (21 bp):
TATATAATATTTTTAAAAAAC
Found at i:1625139 original size:14 final size:14
Alignment explanation
Indices: 1625120--1625148 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1625110 AAGCTATGTT
1625120 GTAAATTAGGTTGA
1 GTAAATTAGGTTGA
1625134 GTAAATTAGGTTGA
1 GTAAATTAGGTTGA
1625148 G
1 G
1625149 AGATAGTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (14 bp):
GTAAATTAGGTTGA
Found at i:1629660 original size:24 final size:24
Alignment explanation
Indices: 1629627--1629690 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
1629617 TCTCCTGCAT
*
1629627 CTTTTGCAGCCGATGAAGCTTGTG
1 CTTTTGCAGCAGATGAAGCTTGTG
* *
1629651 CTTTTACAGCATATGAAGCTTGTG
1 CTTTTGCAGCAGATGAAGCTTGTG
* *
1629675 TTTTTGCAGCATATGA
1 CTTTTGCAGCAGATGA
1629691 GTCTCCTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (24 bp):
CTTTTGCAGCAGATGAAGCTTGTG
Found at i:1631170 original size:15 final size:15
Alignment explanation
Indices: 1631150--1631180 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1631140 GAGCTCTTCA
1631150 TACGACGTCTTTATC
1 TACGACGTCTTTATC
1631165 TACGACGTCTTTATC
1 TACGACGTCTTTATC
1631180 T
1 T
1631181 TGAAGGTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.26, G:0.13, T:0.42
Consensus pattern (15 bp):
TACGACGTCTTTATC
Found at i:1633236 original size:18 final size:17
Alignment explanation
Indices: 1633201--1633247 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
1633191 TAAAAAAGTC
1633201 AAAAATAAATATAAATA
1 AAAAATAAATATAAATA
*
1633218 ATAAAATAAATCA-AGATA
1 A-AAAATAAAT-ATAAATA
1633236 AAAGAATAAATA
1 AAA-AATAAATA
1633248 CAAAGAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 4 0.15
18 21 0.81
19 1 0.04
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.21
Consensus pattern (17 bp):
AAAAATAAATATAAATA
Found at i:1633291 original size:5 final size:5
Alignment explanation
Indices: 1633276--1633340 Score: 57
Period size: 5 Copynumber: 13.2 Consensus size: 5
1633266 GTTAGAATAA
* *
1633276 AAATAT AAATT AAATT AAATAA AAAAT AAATT AAATT AAA-- AAATT AAATT
1 AAAT-T AAATT AAATT AAAT-T AAATT AAATT AAATT AAATT AAATT AAATT
1633326 AAA-- AAGATT AAATT A
1 AAATT AA-ATT AAATT A
1633341 GAAAGAATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
3 5 0.10
4 1 0.02
5 34 0.69
6 9 0.18
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (5 bp):
AAATT
Found at i:1633304 original size:21 final size:22
Alignment explanation
Indices: 1633271--1633315 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 22
1633261 TTAGGGTTAG
1633271 AATAAAAATATAAATTAAATTA
1 AATAAAAATATAAATTAAATTA
1633293 AATAAAAA-ATAAATTAAATTA
1 AATAAAAATATAAATTAAATTA
1633314 AA
1 AA
1633316 AAATTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
AATAAAAATATAAATTAAATTA
Found at i:1633305 original size:16 final size:16
Alignment explanation
Indices: 1633276--1633328 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
1633266 GTTAGAATAA
* *
1633276 AAATATAAATTAAATT
1 AAATAAAAAATAAATT
1633292 AAATAAAAAATAAATT
1 AAATAAAAAATAAATT
1633308 AAATTAAAAAATTAAATT
1 AAA-TAAAAAA-TAAATT
1633326 AAA
1 AAA
1633329 AAGATTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
16 17 0.52
17 7 0.21
18 9 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAAAAAATAAATT
Found at i:1633319 original size:29 final size:28
Alignment explanation
Indices: 1633287--1633352 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
1633277 AATATAAATT
1633287 AAATTAAATAAAAAATAAATTAAATTA-AA
1 AAATTAAAT-AAAAA-AAATTAAATTAGAA
* *
1633316 AAATTAAATTAAAAAGATTAAATTAGAA
1 AAATTAAATAAAAAAAATTAAATTAGAA
1633344 AGAATTAAA
1 A-AATTAAA
1633353 ATCAAGAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 10 0.30
28 7 0.21
29 16 0.48
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (28 bp):
AAATTAAATAAAAAAAATTAAATTAGAA
Found at i:1633335 original size:14 final size:14
Alignment explanation
Indices: 1633305--1633352 Score: 71
Period size: 13 Copynumber: 3.4 Consensus size: 14
1633295 TAAAAAATAA
1633305 ATTAAATTAAAAA-
1 ATTAAATTAAAAAG
1633318 ATTAAATTAAAAAG
1 ATTAAATTAAAAAG
*
1633332 ATTAAATTAGAAAG
1 ATTAAATTAAAAAG
1633346 AATTAAA
1 -ATTAAA
1633353 ATCAAGAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 13 0.41
14 13 0.41
15 6 0.19
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (14 bp):
ATTAAATTAAAAAG
Found at i:1634692 original size:5 final size:5
Alignment explanation
Indices: 1634684--1635348 Score: 1031
Period size: 5 Copynumber: 132.6 Consensus size: 5
1634674 AAAGAAAACC
1634684 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1634734 ATAAT ATAAT ATAAT AT-A- ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1634782 ATAAT ATAAT AT-A- ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1634830 AT-A- ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1634877 ATAAT AT-AT AT-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1634925 ATAATAT ATAAT ATAAT ATAAT ATAAT AT-AT ATAAT ATAATAT ATAAT
1 AT-A-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-A-AT ATAAT
1634973 ATAAT ATAAT ATAAT AT-AT A-ATAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT
1635022 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAATAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-A-AT ATAAT ATAAT
1635074 ATAAT ATAAT ATAAT ATATAT ATAA- AT-AT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1635123 ATAATAT ATAAT ATAAT ATAAT ATAAT AT-AT ATAAT ATAAT ATAAT ATAAT
1 AT-A-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1635174 ATAAT ATAAT ATAATAT ATAAT ATAAT ATAAT AT-AT ATAAT ATAAT ATAAT
1 ATAAT ATAAT AT-A-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1635225 AATATAT ATAAT A-AAT ATAAT ATAAT ATAAT ATATAT ATAAT ATAAT
1 -ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT
1635272 ATAAT ATAAT ATAAT ATAAT ATAATAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT AT-A-AT ATAAT ATAAT ATAAT ATAAT ATAAT
*
1635324 ATATAT AATAAT ATAAC ATAAT ATA
1 ATA-AT -ATAAT ATAAT ATAAT ATA
1635349 TATTTATTTA
Statistics
Matches: 623, Mismatches: 2, Indels: 70
0.90 0.00 0.10
Matches are distributed among these distances:
3 7 0.01
4 41 0.07
5 513 0.82
6 33 0.05
7 29 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:1635367 original size:29 final size:29
Alignment explanation
Indices: 1635308--1635396 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 29
1635298 TATAATATAA
* * * *
1635308 TATAATATAATATA-ATATATATAATAA-
1 TATAACATAATATATATTTATTTAAAAAC
1635335 TATAACATAATATATATTTATTTAAAAAC
1 TATAACATAATATATATTTATTTAAAAAC
* *
1635364 TATATAACATATTTTATA-TT-TTTAAAAAC
1 --TATAACATAATATATATTTATTTAAAAAC
1635393 TATA
1 TATA
1635397 TAATATGTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
27 17 0.33
28 10 0.19
29 9 0.17
30 2 0.04
31 14 0.27
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (29 bp):
TATAACATAATATATATTTATTTAAAAAC
Found at i:1635397 original size:29 final size:31
Alignment explanation
Indices: 1635334--1635399 Score: 100
Period size: 29 Copynumber: 2.2 Consensus size: 31
1635324 ATATATAATA
1635334 ATATAACATAATATATATTTATTTAAAAACT
1 ATATAACATAATATATATTTATTTAAAAACT
* *
1635365 ATATAACATATTTTATA-TT-TTTAAAAACT
1 ATATAACATAATATATATTTATTTAAAAACT
1635394 ATATAA
1 ATATAA
1635400 TATGTTTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 16 0.48
30 2 0.06
31 15 0.45
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (31 bp):
ATATAACATAATATATATTTATTTAAAAACT
Found at i:1635482 original size:43 final size:41
Alignment explanation
Indices: 1635403--1635483 Score: 128
Period size: 40 Copynumber: 1.9 Consensus size: 41
1635393 TATATAATAT
1635403 GTTTTCAAAAATTATATATATTATATATATTTTCAAAAACC
1 GTTTTCAAAAATTATATATATTATATATATTTTCAAAAACC
1635444 GTTTT-AAAAATTATATATATATATATATATATATTCAAAA
1 GTTTTCAAAAATTATATATAT-TATATATAT-T-TTCAAAA
1635484 TATGTTTTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
40 15 0.41
41 14 0.38
42 1 0.03
43 7 0.19
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.44
Consensus pattern (41 bp):
GTTTTCAAAAATTATATATATTATATATATTTTCAAAAACC
Found at i:1635491 original size:43 final size:41
Alignment explanation
Indices: 1635398--1635509 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 41
1635388 AAAACTATAT
1635398 AATATGTTTTCAAAAATTATATATAT-TATATATATTTTCAA
1 AATATGTTTT-AAAAATTATATATATATATATATATTTTCAA
*
1635439 AA-ACCGTTTTAAAAATTATATATATATATATATATATATTCAA
1 AATA-TGTTTTAAAAATTATATATATATATATATAT-T-TTCAA
* *
1635482 AATATGTTTT-CAAATCTATATTTATATA
1 AATATGTTTTAAAAAT-TATATATATATA
1635510 CTTTTTTAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
40 16 0.26
41 16 0.26
42 5 0.08
43 23 0.38
44 1 0.02
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (41 bp):
AATATGTTTTAAAAATTATATATATATATATATATTTTCAA
Found at i:1635559 original size:36 final size:37
Alignment explanation
Indices: 1635513--1635583 Score: 117
Period size: 38 Copynumber: 1.9 Consensus size: 37
1635503 TTATATACTT
1635513 TTTTAAAAACTG-TTTTTTTAAACTATATATTATATG
1 TTTTAAAAACTGTTTTTTTTAAACTATATATTATATG
*
1635549 TTTTCAAAACTGTTTTTTTTTAAACTATATATTAT
1 TTTTAAAAACTG-TTTTTTTTAAACTATATATTAT
1635584 TTCAAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 11 0.34
38 21 0.66
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.55
Consensus pattern (37 bp):
TTTTAAAAACTGTTTTTTTTAAACTATATATTATATG
Found at i:1637717 original size:53 final size:54
Alignment explanation
Indices: 1637642--1637749 Score: 173
Period size: 53 Copynumber: 2.0 Consensus size: 54
1637632 TTCACCATAA
1637642 ACCCGAACCCGACCCGAATATCACAC-TAAAAAAACCCAACCCAACCCGACCCG
1 ACCCGAACCCGACCCGAATATCACACTTAAAAAAACCCAACCCAACCCGACCCG
* * * *
1637695 ACCCGAACCCTACCCGAATATCACACTTACAAAAACCCGACCCGACCCGACCCG
1 ACCCGAACCCGACCCGAATATCACACTTAAAAAAACCCAACCCAACCCGACCCG
1637749 A
1 A
1637750 ATATTAAACT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
53 25 0.50
54 25 0.50
ACGTcount: A:0.37, C:0.45, G:0.10, T:0.07
Consensus pattern (54 bp):
ACCCGAACCCGACCCGAATATCACACTTAAAAAAACCCAACCCAACCCGACCCG
Found at i:1637767 original size:38 final size:39
Alignment explanation
Indices: 1637690--1637779 Score: 121
Period size: 38 Copynumber: 2.3 Consensus size: 39
1637680 ACCCAACCCG
* *
1637690 ACCCGACCCGAACCCTACCCGAATATCACACTTACAAAA
1 ACCCGACCCGAACCCGACCCGAATATCAAACTTACAAAA
*
1637729 ACCCGACCCG-ACCCGACCCGAATATTAAACTTTA-AAAA
1 ACCCGACCCGAACCCGACCCGAATATCAAAC-TTACAAAA
*
1637767 ACCCGACCTGAAC
1 ACCCGACCCGAAC
1637780 TTGATTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
38 30 0.67
39 15 0.33
ACGTcount: A:0.38, C:0.39, G:0.10, T:0.13
Consensus pattern (39 bp):
ACCCGACCCGAACCCGACCCGAATATCAAACTTACAAAA
Found at i:1637968 original size:24 final size:24
Alignment explanation
Indices: 1637911--1637979 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
1637901 TTTCATTTGA
*
1637911 ATATTATTTA-TATTATTATTATT
1 ATATTATTAATTATTATTATTATT
* *
1637934 ATAATAATAATTATTATTATTATT
1 ATATTATTAATTATTATTATTATT
* * *
1637958 TTATTATTAATAAATATTATTA
1 ATATTATTAATTATTATTATTA
1637980 CAGGCCCAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 7 0.19
24 30 0.81
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATATTATTAATTATTATTATTATT
Found at i:1637968 original size:27 final size:27
Alignment explanation
Indices: 1637921--1637979 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
1637911 ATATTATTTA
*
1637921 TATTATTATTATTATAATAATAATTAT
1 TATTATTATTATTATAATAATAAATAT
*
1637948 TATTATTATT-TTATTATTAATAAATAT
1 TATTATTATTATTA-TAATAATAAATAT
1637975 TATTA
1 TATTA
1637980 CAGGCCCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.10
27 26 0.90
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TATTATTATTATTATAATAATAAATAT
Found at i:1637979 original size:3 final size:3
Alignment explanation
Indices: 1637912--1637966 Score: 60
Period size: 3 Copynumber: 18.7 Consensus size: 3
1637902 TTCATTTGAA
* * *
1637912 TAT TAT T-T ATAT TAT TAT TAT TAT AAT AAT AAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1637957 T-T TAT TAT TA
1 TAT TAT TAT TA
1637967 ATAAATATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 3 0.06
3 43 0.91
4 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1639558 original size:120 final size:120
Alignment explanation
Indices: 1639441--1639673 Score: 303
Period size: 120 Copynumber: 2.0 Consensus size: 120
1639431 ATTTTAATCC
* * * *
1639441 TGTTTTAA-TATTTATTTATTTTTCAATAT-TAAG-AAAGTGCAGTCTTAAAACAACTGGATGTC
1 TGTTTTAATTATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-
* *
1639503 CATTTTCTGATATTTTTAAATTAATAAATATCCTATTTTATAAAT-TATATATTAAT
65 CATTTTCTGATATTTCTAAATAAATAAATATCCTA-TTTATAAATATATATATTAAT
* * ** *
1639559 TGTTTTAATTATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTC
1 TGTTTTAATTATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
**
1639624 ATTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATA
66 ATTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATA
1639674 AATTAATATT
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
118 8 0.08
119 29 0.30
120 40 0.41
121 21 0.21
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.46
Consensus pattern (120 bp):
TGTTTTAATTATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
ATTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATATTAAT
Found at i:1639570 original size:20 final size:19
Alignment explanation
Indices: 1639545--1639586 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1639535 CTATTTTATA
1639545 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
1639565 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
1639584 AAT
1 AAT
1639587 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:1640258 original size:33 final size:33
Alignment explanation
Indices: 1640182--1640265 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 33
1640172 TTCAAATTTT
* *
1640182 TTTATATATA-TACTTA--TTATTTTCATAGTA
1 TTTATATATATTATTTATTTTATTTGCATAGTA
1640212 TTTATATATATTATTTCATTTTATTTGCA-AGTA
1 TTTATATATATTATTT-ATTTTATTTGCATAGTA
*
1640245 TTT-TATTTCATTATTTATTTT
1 TTTATATAT-ATTATTTATTTT
1640266 TCTGTCTGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
30 10 0.22
31 4 0.09
32 10 0.22
33 14 0.30
34 8 0.17
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.62
Consensus pattern (33 bp):
TTTATATATATTATTTATTTTATTTGCATAGTA
Found at i:1643530 original size:15 final size:15
Alignment explanation
Indices: 1643510--1643556 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
1643500 GATCAATACC
1643510 TTTTGCATACATGCA
1 TTTTGCATACATGCA
1643525 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
1643540 TTTTGCATACATTCA
1 TTTTGCATACATGCA
1643555 TT
1 TT
1643557 ATTCATTGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:1650905 original size:8 final size:8
Alignment explanation
Indices: 1650892--1650934 Score: 59
Period size: 8 Copynumber: 5.1 Consensus size: 8
1650882 ATTATGTTTG
1650892 AAGAAAAA
1 AAGAAAAA
1650900 AAGAAAAAAA
1 AAG--AAAAA
1650910 AAGAAAAA
1 AAGAAAAA
*
1650918 AAGAGAAA
1 AAGAAAAA
1650926 AAGAAAAA
1 AAGAAAAA
1650934 A
1 A
1650935 TGAGGGTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 23 0.74
10 8 0.26
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:1650910 original size:10 final size:10
Alignment explanation
Indices: 1650895--1650932 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
1650885 ATGTTTGAAG
1650895 AAAAAAAGAA
1 AAAAAAAGAA
1650905 AAAAAAAGAA
1 AAAAAAAGAA
*
1650915 AAAAAGAGAA
1 AAAAAAAGAA
1650925 AAAGAAAA
1 AAA-AAAA
1650933 AATGAGGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 22 0.88
11 3 0.12
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:1650915 original size:18 final size:19
Alignment explanation
Indices: 1650892--1650927 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1650882 ATTATGTTTG
1650892 AAGAAAAAAAGA-AAAAAA
1 AAGAAAAAAAGAGAAAAAA
1650910 AAGAAAAAAAGAGAAAAA
1 AAGAAAAAAAGAGAAAAA
1650928 GAAAAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (19 bp):
AAGAAAAAAAGAGAAAAAA
Found at i:1651334 original size:19 final size:18
Alignment explanation
Indices: 1651288--1651336 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
1651278 TATTTTCTCT
1651288 AAATTCAATTTA--TTTG
1 AAATTCAATTTATTTTTG
* *
1651304 AGATTCATTTTATTTTTG
1 AAATTCAATTTATTTTTG
1651322 AAAATTCAATTTATT
1 -AAATTCAATTTATT
1651337 CTTTTATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 10 0.38
18 4 0.15
19 12 0.46
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (18 bp):
AAATTCAATTTATTTTTG
Found at i:1652695 original size:113 final size:112
Alignment explanation
Indices: 1652497--1653270 Score: 1052
Period size: 113 Copynumber: 6.9 Consensus size: 112
1652487 ATCCATCACA
* *
1652497 ATGGATCAGCTTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAA-AAGAA
1 ATGGATCAGCATTGCCAGTAG--AGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAAGAAGAA
* * * *
1652560 GTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
63 GTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCG
* * * *
1652610 ATGGATCAGCTTTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAGCATTGCCAGTA-GAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGT
* *
1652675 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTG
65 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCG
* * *
1652723 ATAGATCAACATTGCCAAGTAGAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAAGAAGAAGT
1 ATGGATCAGCATTGCC-AGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGT
* *
1652788 TCATAATGAGAATAACTTGTTCAACTTTTTGCTTAAATTCATCACTCG
65 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCG
* * * * *
1652836 GTGGATCAACAATGCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTT
1 ATGGATCAGCATTGCCAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTT
*
1652901 CATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCG
66 CATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCG
* * *
1652948 GTGGATCAGCAATGCCAGTTAGAATTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGT
1 ATGGATCAGCATTGCCAG-TAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGT
* * *
1653013 TTATAATGAGAAGAACTTGTTTAACGTTTTGCTTAAATTCATCACTCG
65 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCG
* * *
1653061 GTGGATCAGCAATGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAAT
1 ATGGATCAGCATTGCCAG-TAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGT
* *
1653126 TCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTG
65 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCG
* * * * *
1653174 ATGGATCA-AATTTTCCAG-AGAAAGTTCAGAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAA
1 ATGGATCAGCA-TTGCCAGTAG--AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAA
* * *
1653237 GTTAATAATGAGAAGAGCTTGTTCGACCTTTTGC
63 GTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
1653271 ATGACTCTAT
Statistics
Matches: 604, Mismatches: 49, Indels: 16
0.90 0.07 0.02
Matches are distributed among these distances:
111 2 0.00
112 113 0.19
113 484 0.80
114 4 0.01
115 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (112 bp):
ATGGATCAGCATTGCCAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTT
CATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCG
Found at i:1653136 original size:338 final size:339
Alignment explanation
Indices: 1652511--1653270 Score: 1116
Period size: 338 Copynumber: 2.2 Consensus size: 339
1652501 ATCAGCTTTT
1652511 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAA-AAGAAGTTCATAATGAGAAG
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAAGAAGAAGTTCATAATGAGAAG
* ** * *
1652575 AGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAGGAGTTCATA
65 AGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAGCAATGCCAGAAGGAATTCATA
*
1652640 ATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
130 ATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
* * *
1652705 GCTTGAATTCATCACTTGATAGATCAACATTGCCAAGTAGAGTTCATAATAAGAAGAACTCATCT
195 GCTTAAATTCATCACTCGATAGATCAACAATGCCAAGTAGAGTTCATAATAAGAAGAACTCATCT
* * *
1652770 GAAGAAGAAAGAAGAAGTTCATAATGAGAATAACTTGTTCAACTTTTTGCTTAAATTCATCACTC
260 GAAGAAGAAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTC
*
1652835 GGTGGATCAACA-ATG
325 GATGGATCAA-ATATG
**
1652850 CCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGA
* * * * * *
1652914 ACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAGCAATGCCAGTTA-GAATTCATA
66 GCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAGCAATGCCAG-AAGGAATTCATA
* * *
1652978 ATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTTATAATGAGAAGAACTTGTTTAACGTTTT
130 ATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
* * * *
1653043 GCTTAAATTCATCACTCGGTGGATCAGCAATGCC-AGTTAGAGTTCATAATGAGAAGAACTCATC
195 GCTTAAATTCATCACTCGATAGATCAACAATGCCAAG-TAGAGTTCATAATAAGAAGAACTCATC
*
1653107 TGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACT
259 TGAAGAAGAAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACT
* * *
1653172 TGATGGATCAAATTTT
324 CGATGGATCAAATATG
* * * *
1653188 CCAGAGAAAGTTCAGAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTAATAATGAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGA
*
1653253 GCTTGTTCGACCTTTTGC
66 GCTTGTTCAACCTTTTGC
1653271 ATGACTCTAT
Statistics
Matches: 375, Mismatches: 41, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
337 7 0.02
338 294 0.78
339 74 0.20
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (339 bp):
CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGA
GCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAGCAATGCCAGAAGGAATTCATAA
TGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
CTTAAATTCATCACTCGATAGATCAACAATGCCAAGTAGAGTTCATAATAAGAAGAACTCATCTG
AAGAAGAAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCG
ATGGATCAAATATG
Found at i:1653666 original size:3 final size:3
Alignment explanation
Indices: 1653608--1653653 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
1653598 TTCATTTGAA
1653608 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1653652 TA
1 TA
1653654 ATAAATATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 3 0.08
3 36 0.90
4 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1655273 original size:20 final size:19
Alignment explanation
Indices: 1655248--1655289 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1655238 CTATTTTATA
1655248 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
1655268 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
1655287 AAT
1 AAT
1655290 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:1655285 original size:119 final size:117
Alignment explanation
Indices: 1655144--1655380 Score: 298
Period size: 120 Copynumber: 2.0 Consensus size: 117
1655134 ATTTTAATCC
* * * *
1655144 TGTTTTAATATTTATTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTTAAAACAACTGGATGTCT
1 TGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC-
* * *
1655207 ATTTTCTGATATTTTTAAATTAATAAATATCCTATTTTATAAATTATATATTAAT
65 ATTTTCTGATATTTCTAAATAAATAAATATCCTA-TTTATAAA-TATATATAAAT
* * ** *
1655262 TGTTTTAATTATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTC
1 TGTTTTAA-TATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
**
1655327 ATTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAAT
65 ATTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAAT
1655380 T
1 T
1655381 AATATTTTTT
Statistics
Matches: 102, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
118 19 0.19
119 28 0.27
120 33 0.32
121 22 0.22
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.46
Consensus pattern (117 bp):
TGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCA
TTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAAT
Found at i:1657158 original size:16 final size:16
Alignment explanation
Indices: 1657137--1657178 Score: 77
Period size: 15 Copynumber: 2.7 Consensus size: 16
1657127 AAACTCACCA
1657137 ATTTTTTTTATCTTAT
1 ATTTTTTTTATCTTAT
1657153 A-TTTTTTTATCTTAT
1 ATTTTTTTTATCTTAT
1657168 ATTTTTTTTAT
1 ATTTTTTTTAT
1657179 ATGAAATGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 15 0.60
16 10 0.40
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTTTTTTATCTTAT
Found at i:1658851 original size:15 final size:15
Alignment explanation
Indices: 1658815--1658864 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
1658805 GTGAAATTCT
*
1658815 AATTATTTAAATAAA
1 AATTATTTATATAAA
1658830 TAATTATTTATATAAA
1 -AATTATTTATATAAA
1658846 AATTATTTATATAAA
1 AATTATTTATATAAA
1658861 AATT
1 AATT
1658865 CATCGATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 19 0.58
16 14 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTATTTATATAAA
Found at i:1658874 original size:41 final size:41
Alignment explanation
Indices: 1658829--1658920 Score: 150
Period size: 41 Copynumber: 2.2 Consensus size: 41
1658819 ATTTAAATAA
* *
1658829 ATAAT-TATTTATATAAAAATTATTTATATAAAAATTCATCG
1 ATAATATATTTAAATAAAAA-CATTTATATAAAAATTCATCG
1658870 ATAATATATTTAAATAAAAACATTTATATAAAAATTCATCG
1 ATAATATATTTAAATAAAAACATTTATATAAAAATTCATCG
1658911 ATAATATATT
1 ATAATATATT
1658921 ATTTAAATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
41 35 0.73
42 13 0.27
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (41 bp):
ATAATATATTTAAATAAAAACATTTATATAAAAATTCATCG
Found at i:1658900 original size:27 final size:26
Alignment explanation
Indices: 1658814--1658900 Score: 61
Period size: 27 Copynumber: 3.1 Consensus size: 26
1658804 AGTGAAATTC
1658814 TAAT-TATTTAAATAAATAATTATTTATA
1 TAATATATTTAAATAAA-AA--ATTTATA
* * *
1658842 TAAAAATTATTTATAT-AAAAATTCATCGA
1 T-AATA-TATTTAAATAAAAAATTTAT--A
1658871 TAATATATTTAAATAAAAACATTTATA
1 TAATATATTTAAATAAAAA-ATTTATA
1658898 TAA
1 TAA
1658901 AAATTCATCG
Statistics
Matches: 46, Mismatches: 6, Indels: 15
0.69 0.09 0.22
Matches are distributed among these distances:
27 17 0.37
28 8 0.17
29 11 0.24
30 2 0.04
31 8 0.17
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (26 bp):
TAATATATTTAAATAAAAAATTTATA
Found at i:1660611 original size:33 final size:33
Alignment explanation
Indices: 1660569--1660639 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1660559 GGAAATACTA
*
1660569 AATCTGTAGTTCAGTTGAATTATCATAAATCAT
1 AATCTGTAGTTCAGTTGAATTATCATAAATAAT
*
1660602 AATCTGTAGTTCAGTTTAATTATCATAAATAAT
1 AATCTGTAGTTCAGTTGAATTATCATAAATAAT
1660635 AATCT
1 AATCT
1660640 TGGTCAGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (33 bp):
AATCTGTAGTTCAGTTGAATTATCATAAATAAT
Found at i:1661390 original size:8 final size:9
Alignment explanation
Indices: 1661362--1661394 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
1661352 CTGAACAACG
1661362 AAATCGAGA
1 AAATCGAGA
1661371 AAATCGAGA
1 AAATCGAGA
1661380 AAATCGA-A
1 AAATCGAGA
1661388 AAATCGA
1 AAATCGA
1661395 TACGAATCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.58, C:0.12, G:0.18, T:0.12
Consensus pattern (9 bp):
AAATCGAGA
Found at i:1662125 original size:14 final size:13
Alignment explanation
Indices: 1662106--1662134 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1662096 AAAAATTTCT
1662106 TTAAAAACTATCA
1 TTAAAAACTATCA
1662119 TTAAAAACTATCA
1 TTAAAAACTATCA
1662132 TTA
1 TTA
1662135 TTATGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (13 bp):
TTAAAAACTATCA
Found at i:1662722 original size:46 final size:45
Alignment explanation
Indices: 1662655--1662773 Score: 157
Period size: 36 Copynumber: 2.8 Consensus size: 45
1662645 CACTCGGGGC
1662655 TCGGTTCATGCATGGGGCACTCGAGGCGACCAAGGATGACCAAGGA
1 TCGGTTCATGCATGGGGCACTCG-GGCGACCAAGGATGACCAAGGA
1662701 TCGGTTCATGCATGGGGCACTCGGG-G--C------GACCAAGGA
1 TCGGTTCATGCATGGGGCACTCGGGCGACCAAGGATGACCAAGGA
1662737 TCGGTTCATGCATGGGGCACTCGGGGCGACCAAGGAT
1 TCGGTTCATGCATGGGGCACTC-GGGCGACCAAGGAT
1662774 CGGTTCATGC
Statistics
Matches: 63, Mismatches: 0, Indels: 20
0.76 0.00 0.24
Matches are distributed among these distances:
36 31 0.49
37 3 0.05
38 1 0.02
40 1 0.02
42 1 0.02
44 1 0.02
45 2 0.03
46 23 0.37
ACGTcount: A:0.22, C:0.24, G:0.37, T:0.17
Consensus pattern (45 bp):
TCGGTTCATGCATGGGGCACTCGGGCGACCAAGGATGACCAAGGA
Found at i:1662798 original size:36 final size:36
Alignment explanation
Indices: 1662692--1662788 Score: 194
Period size: 36 Copynumber: 2.7 Consensus size: 36
1662682 GACCAAGGAT
1662692 GACCAAGGATCGGTTCATGCATGGGGCACTCGGGGC
1 GACCAAGGATCGGTTCATGCATGGGGCACTCGGGGC
1662728 GACCAAGGATCGGTTCATGCATGGGGCACTCGGGGC
1 GACCAAGGATCGGTTCATGCATGGGGCACTCGGGGC
1662764 GACCAAGGATCGGTTCATGCATGGG
1 GACCAAGGATCGGTTCATGCATGGG
1662789 AAGAACGGGG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.21, C:0.24, G:0.38, T:0.18
Consensus pattern (36 bp):
GACCAAGGATCGGTTCATGCATGGGGCACTCGGGGC
Found at i:1662898 original size:29 final size:29
Alignment explanation
Indices: 1662865--1662949 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
1662855 AGCAGGGGAT
* * **
1662865 GTCGCCGCGAGTGCATGGCGACCTCCTTG
1 GTCGCCGAGAGTGCATGGCGACCTACGAG
* *
1662894 GTCGCCGAGCGTGCATGGCGACCTAGGAG
1 GTCGCCGAGAGTGCATGGCGACCTACGAG
* *
1662923 GTCGCTGGGAGTGCATGGCGACCTACG
1 GTCGCCGAGAGTGCATGGCGACCTACG
1662950 GCTACTGTTA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.14, C:0.29, G:0.39, T:0.18
Consensus pattern (29 bp):
GTCGCCGAGAGTGCATGGCGACCTACGAG
Found at i:1664057 original size:20 final size:20
Alignment explanation
Indices: 1664034--1664085 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1664024 AACGCGATCC
1664034 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
1664054 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
1664074 CCAAAATCGCAA
1 CCAGAATCGCAA
1664086 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:1664166 original size:20 final size:20
Alignment explanation
Indices: 1664141--1664334 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
1664131 GATTTTCCAT
* *
1664141 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
1664161 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
1664181 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1664201 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
1664221 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
1664241 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1664261 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
1664281 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
1664302 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
1664322 AATCGCAACGCGA
1 AATCGCAACGCGA
1664335 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:1664186 original size:40 final size:39
Alignment explanation
Indices: 1664137--1664334 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
1664127 TTGCGATTTT
* ** *
1664137 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
1664175 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
1664216 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
1664256 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
1664295 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1664335 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:1664224 original size:60 final size:60
Alignment explanation
Indices: 1664141--1664333 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1664131 GATTTTCCAT
* ** * *
1664141 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
1664201 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
1664261 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
1664322 AATCGCAACGCG
1 AATCGCAACGCG
1664334 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:1664754 original size:33 final size:33
Alignment explanation
Indices: 1664715--1664785 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1664705 TTCACTTAGA
*
1664715 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1664748 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1664781 TTTCA
1 TTTCA
1664786 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1664925 original size:14 final size:14
Alignment explanation
Indices: 1664906--1664960 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1664896 AGAATGACTG
1664906 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
1664920 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
1664939 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1664953 TCGCAACG
1 TCGCAACG
1664961 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:1664943 original size:33 final size:33
Alignment explanation
Indices: 1664906--1664976 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1664896 AGAATGACTG
**
1664906 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1664939 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1664972 TCGCA
1 TCGCA
1664977 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:1664994 original size:19 final size:19
Alignment explanation
Indices: 1664972--1665069 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1664962 GAAACCAAAA
*
1664972 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1664991 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1665005 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1665024 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1665038 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
1665057 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1665070 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1665013 original size:14 final size:14
Alignment explanation
Indices: 1664994--1665083 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1664984 TTTCATTTCG
1664994 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1665008 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1665027 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1665041 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1665058 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1665074 CGTTGCGATT
1 CGTTGCGATT
1665084 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1665019 original size:33 final size:33
Alignment explanation
Indices: 1664977--1665091 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1664967 CAAAATCGCA
1664977 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1665010 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1665043 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1665076 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1665092 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1667098 original size:184 final size:186
Alignment explanation
Indices: 1666789--1667254 Score: 909
Period size: 184 Copynumber: 2.5 Consensus size: 186
1666779 TAGATTGCTT
*
1666789 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1666854 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1666919 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTG-TTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1666973 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1667038 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1667103 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1667159 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1667224 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
1667255 TTCAATTTGC
Statistics
Matches: 279, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
184 154 0.55
185 12 0.04
186 113 0.41
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1667115 original size:93 final size:93
Alignment explanation
Indices: 1666789--1667254 Score: 909
Period size: 93 Copynumber: 5.0 Consensus size: 93
1666779 TAGATTGCTT
*
1666789 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1666854 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1666882 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1666946 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1666973 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1667038 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1667066 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1667131 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1667159 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1667224 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1667252 AGT
1 AGT
1667255 TTCAATTTGC
Statistics
Matches: 370, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
91 79 0.21
92 24 0.06
93 267 0.72
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1667326 original size:19 final size:19
Alignment explanation
Indices: 1667286--1667414 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1667276 TAGTTTACTT
* *
1667286 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1667306 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1667325 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1667344 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1667358 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1667377 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1667391 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1667410 TCGCA
1 TCGCA
1667415 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1667365 original size:33 final size:32
Alignment explanation
Indices: 1667322--1667414 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1667312 CGCGAAACCA
**
1667322 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1667354 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1667387 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1667415 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1667412 original size:52 final size:52
Alignment explanation
Indices: 1667286--1667414 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1667276 TAGTTTACTT
**
1667286 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1667338 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1667391 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1667415 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1667432 original size:19 final size:19
Alignment explanation
Indices: 1667410--1667544 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1667400 GAAACCAAAA
*
1667410 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1667429 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1667445 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1667462 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1667478 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1667495 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1667514 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1667534 TCGTGTTGCGA
1 TCGCGTTGCGA
1667545 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1667451 original size:14 final size:14
Alignment explanation
Indices: 1667432--1667488 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1667422 TTTCATTTCG
1667432 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1667446 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1667463 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1667479 CGTTGCGATT
1 CGTTGCGATT
1667489 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1667457 original size:33 final size:33
Alignment explanation
Indices: 1667415--1667507 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1667405 CAAAATCGCA
*
1667415 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1667448 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1667481 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1667508 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1669486 original size:14 final size:14
Alignment explanation
Indices: 1669467--1669502 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1669457 ATTGTTTAAT
1669467 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1669481 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1669495 TGATTTGT
1 TGATTTGT
1669503 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1669625 original size:19 final size:19
Alignment explanation
Indices: 1669609--1669710 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1669599 AAAAATGACT
1669609 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1669628 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1669647 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1669661 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1669680 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1669700 ATCGCAATGCG
1 ATCGCAATGCG
1669711 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1669759 original size:33 final size:36
Alignment explanation
Indices: 1669717--1670030 Score: 291
Period size: 33 Copynumber: 9.1 Consensus size: 36
1669707 TGCGTTTATA
*
1669717 ATTTCGCATTGCGA-TT-ATCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
1669750 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
1669786 -TTTCG--TTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
1669819 -TTTCG--TTGCGATTTTCATTTCGCATTGCGA-TTTA
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
1669853 ATTTCGCATTGCGA-TTC-TGTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
1669886 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
1669924 ATTTCGCATTGCGA-TTC-TCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
1669957 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
1669993 -TCTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTCATTT-CG-ATTGCGATTTTC
1670029 AT
1 AT
1670031 GTTGGGATTT
Statistics
Matches: 249, Mismatches: 8, Indels: 44
0.83 0.03 0.15
Matches are distributed among these distances:
32 6 0.02
33 129 0.52
34 16 0.06
35 29 0.12
36 25 0.10
37 7 0.03
38 37 0.15
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (36 bp):
ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
Found at i:1669763 original size:19 final size:19
Alignment explanation
Indices: 1669739--1670058 Score: 360
Period size: 19 Copynumber: 18.4 Consensus size: 19
1669729 GATTATCTCG
1669739 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1669758 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1669777 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1669791 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1669810 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1669824 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1669843 TTGCGA-TTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1669861 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
1669875 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1669894 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1669913 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1669932 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1669946 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1669965 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1669984 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1669998 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1670018 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1670032 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1670051 TTGCGATT
1 TTGCGATT
1670059 GTATTTTCCG
Statistics
Matches: 260, Mismatches: 10, Indels: 62
0.78 0.03 0.19
Matches are distributed among these distances:
14 41 0.16
16 39 0.15
17 35 0.13
18 20 0.08
19 113 0.43
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1669779 original size:52 final size:52
Alignment explanation
Indices: 1669717--1670030 Score: 403
Period size: 52 Copynumber: 6.0 Consensus size: 52
1669707 TGCGTTTATA
*
1669717 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1669769 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
1669819 -TTTCG--TTGCGATTTTCATTTCGCATTGCGA-TTTAATTTCGCATTGCGATTCTGTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATT-T-TC
* * * * *
1669874 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1669924 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1669976 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
1670029 AT
1 AT
1670031 GTTGGGATTT
Statistics
Matches: 231, Mismatches: 14, Indels: 33
0.83 0.05 0.12
Matches are distributed among these distances:
47 6 0.03
49 8 0.03
50 17 0.07
51 28 0.12
52 140 0.61
53 19 0.08
54 1 0.00
55 4 0.02
56 4 0.02
57 1 0.00
58 3 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1672355 original size:12 final size:12
Alignment explanation
Indices: 1672338--1672362 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1672328 TCTTCGGGGA
1672338 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1672350 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1672362 C
1 C
1672363 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1672571 original size:24 final size:24
Alignment explanation
Indices: 1672537--1672583 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1672527 CTGAAACATC
1672537 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1672561 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1672584 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Done.